3TA (was Human and ape phylogeny)

Richard Jensen rjensen at SAINTMARYS.EDU
Wed Apr 9 13:19:48 CDT 2003

A phenetic classification is a hypothesis about natural relationships.  What are
the relationships among A ,B and C?  Our initial data set yields (A(B,C)).  We
"discover" a new set of characters that we believe will help clarify the
relationships.  We include these with our initial data and the answer is (A(B,C)).
Thus, our initial hypothesis has been tested against the new information and has
been found to be consistent with the new information (or, at the least, the new set
of characters did not have a strong enough signal to alter the result).  Of course,
one could argue that the 250 characters in our first data set completely swamped
the signal in the 10 newly discovered characters, but that's another matter
entirely.  The second result is based on total evidence and we have no reason to
question our hypothesis that (B,C) is a natural group with respect to A.



pierre deleporte wrote:

> Thanks to Richard Jensen to confirm that phenetics were not intended as
> phylogenetic in the first place, and that they can perfectly be performed
> under different assumptions "e.g., including or ignoring negative matches
> when calculating association coefficients".
> The proponents of 3TA generally deny this last point, oddly believing that
> phenetics obligatorily accept to group on the basis of negative matches,
> i.e. shared absence. They confound a characteristic of some options of
> phenetics with the method itself. They are eager "not to be phenetic", but
> they are satisfied in this respect when they group on positive matches
> only. Trained pheneticians will appreciate.
> Of course phenetic analysis can fit some models of character evolution
> (typically clocklike evolution implying regular divergence), and of course
> the availability of a number of options is not a flaw in itself in any
> method (phylogenetic methods involve as many otions as evolutionary models).
> The question is just not to forget arguing the choice of the option. If you
> get puzzled when the moment comes to argue your choice of options, you must
> severely question your problematic: which tool is best for which task in
> which theoretical framework ?
> I just don't grasp the notion of "testable hypothesis of relationships"
> raised by Jensen, but this is another question.
> Phenetics infer an optimal phenogram from a data matrix using some option,
> and that's it. There's no test involved.
> You can of course deal with another data matrix or another option. There's
> still no test involved.
> You can also have two data matrices involving different character sets for
> the same set of taxa. Just combine them in one data matrix and draw the
> phenogram. No test involved either.
> What are phenetic tests, if any?
> best,
> Pierre
> A 08:21 09/04/2003 -0500, Richard Jensen wrote :
> >I can't help but think that phenetics is getting a bad rap here.  Phenetic
> >analyses make no reference to apomorphic, plesiomorphic, synapomorphic, etc.
> >with respect to characters.  Characters provide the information by which the
> >analysis is conducted and a phenetic analysis will lead to a classification.
> >And, it is a testable hypothesis of relationships.
> >
> >Sokal and Sneath never intended for phenetic analyses to be interpreted as
> >phylogenetic or evolutionary classifications.  Colless noted that, with
> >certain
> >assumptions, phenetic analyses would be expected to be good approxamations to
> >such releationships and it has been suggested that in situations in which
> >there
> >is little homoplasy, phenetic analyses and cladistic analyses may yield
> >the same
> >"solution."  And, despite the appearance of phenograms as trees, they
> >cannot be
> >interpreted as rooted trees.  They represent sets and subsets in a nested
> >fashion.
> >
> >Further, don't criticize phenetics for the many options available for
> >conducting
> >phenetic analyses.  Unless I have missed something important over the last 20
> >years, there are a variety of approaches for conducting cladistic analyses and
> >they typically yield different results for a single data matrix.  In other
> >words, both approaches yield results that are dependent on a set of
> >choices made
> >by the investigator.  The fundamental question is whether or not the choices
> >made can be justified (e.g., including or ignoring negative matches when
> >calculating association coefficients).
> >
> >Dick
> >
> >pierre deleporte wrote:
> >
> > > Hi René, David, and taxacomers
> > >
> >(...)
> Pierre Deleporte
> CNRS UMR 6552 - Station Biologique de Paimpont
> F-35380 Paimpont   FRANCE
> Téléphone : 02 99 61 81 66
> Télécopie : 02 99 61 81 88

Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen

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